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the workflow and CI system for my GitHub 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bash\nset -euo pipefail\n\nLOG_PREFIX=\"[workflows-codex-env]\"\nlog() { printf \"%s %s\\n\" \"$LOG_PREFIX\" \"$*\"; }\nwarn() { printf \"%s [warn] %s\\n\" \"$LOG_PREFIX\" \"$*\" >&2; }\ndie() { printf \"%s [error] %s\\n\" \"$LOG_PREFIX\" \"$*\" >&2; exit 1; }\n\n# -----------------------------\n# Locate Workflows repo root robustly (Codex scripts run from /tmp)\n# -----------------------------\nis_workflows_root() {\n local d=\"$1\"\n [[ -f \"${d}/pyproject.toml\" ]] || return 1\n [[ -f \"${d}/scripts/dev_check.sh\" ]] || return 1\n grep -q 'name = \"workflows\"' \"${d}/pyproject.toml\" 2>/dev/null || return 1\n return 0\n}\n\nfind_repo_root() {\n # 1) Prefer git root, but verify it's the Workflows repo.\n if command -v git >/dev/null 2>&1; then\n if git rev-parse --show-toplevel >/dev/null 2>&1; then\n local gr\n gr=\"$(git rev-parse --show-toplevel)\"\n if is_workflows_root \"${gr}\"; then\n echo \"${gr}\"\n return 0\n fi\n fi\n fi\n\n # 2) Walk upwards from current directory.\n local d=\"${PWD}\"\n while [[ \"${d}\" != \"/\" ]]; do\n if is_workflows_root \"${d}\"; then\n echo \"${d}\"\n return 0\n fi\n d=\"$(dirname \"${d}\")\"\n done\n\n # 3) Last resort: search common mount points.\n local bases=(\"${PWD}\" \"${GITHUB_WORKSPACE:-}\" \"/workspace\" \"/repo\" \"${HOME:-/home}\" \"/tmp\")\n local b\n for b in \"${bases[@]}\"; do\n [[ -n \"${b}\" && -d \"${b}\" ]] || continue\n while IFS= read -r py; do\n local cand\n cand=\"$(cd \"$(dirname \"${py}\")\" && pwd)\"\n if is_workflows_root \"${cand}\"; then\n echo \"${cand}\"\n return 0\n fi\n done < <(find \"${b}\" -maxdepth 5 -type f -name pyproject.toml 2>/dev/null | head -n 100)\n done\n\n return 1\n}\n\nREPO_ROOT=\"$(find_repo_root || true)\"\n[[ -n \"${REPO_ROOT}\" ]] || die \"Could not locate Workflows repo root (pyproject.toml + scripts/dev_check.sh + name='workflows').\"\n\ncd \"${REPO_ROOT}\"\nlog \"Repo root: ${REPO_ROOT}\"\n\n# Git sanity (best-effort)\nif command -v git >/dev/null 2>&1; then\n git config --global --add safe.directory \"${REPO_ROOT}\" >/dev/null 2>&1 || true\n git config --global user.name \"${GIT_AUTHOR_NAME:-Codex}\" >/dev/null 2>&1 || true\n git config --global user.email \"${GIT_AUTHOR_EMAIL:-codex@users.noreply.github.com}\" >/dev/null 2>&1 || true\nfi\n\n# -----------------------------\n# Python + venv (repo requires 3.11+)\n# -----------------------------\nPYTHON_BIN=\"${PYTHON_BIN:-python3}\"\ncommand -v \"${PYTHON_BIN}\" >/dev/null 2>&1 || die \"python3 not found on PATH.\"\n\n\"${PYTHON_BIN}\" - <<'PY'\nimport sys\nif sys.version_info < (3, 11):\n raise SystemExit(f\"Python 3.11+ required; found {sys.version.split()[0]}\")\nprint(\"Python OK:\", sys.version.split()[0])\nPY\n\nVENV_PATH=\"${REPO_ROOT}/.venv\"\nif [[ ! -d \"${VENV_PATH}\" ]]; then\n log \"Creating venv at ${VENV_PATH}\"\n \"${PYTHON_BIN}\" -m venv \"${VENV_PATH}\"\nfi\n# shellcheck disable=SC1091\nsource \"${VENV_PATH}/bin/activate\"\n\npython -m pip install -U pip setuptools wheel >/dev/null\n\n# -----------------------------\n# Optional lockfile sync (if present)\n# -----------------------------\npython -m pip install -U uv >/dev/null || true\n\nLOCK_FILE=\"${REPO_ROOT}/requirements.lock\"\nif [[ -f \"${LOCK_FILE}\" ]]; then\n log \"Found requirements.lock; syncing with uv (best-effort)\"\n uv pip sync \"${LOCK_FILE}\" || true\nelse\n log \"No requirements.lock found (expected for this repo).\"\nfi\n\n# -----------------------------\n# Install pyproject dependencies + dev extras WITHOUT installing the repo itself\n# (Avoids editable-build failure due to flat-layout multiple top-level packages.)\n# -----------------------------\nlog \"Installing deps + dev tools from pyproject.toml (no editable install)...\"\npython - <<'PY'\nfrom __future__ import annotations\nfrom pathlib import Path\nimport subprocess, sys\n\ntry:\n import tomllib # py3.11+\nexcept ModuleNotFoundError:\n subprocess.check_call([sys.executable, \"-m\", \"pip\", \"install\", \"tomli\"])\n import tomli as tomllib # type: ignore\n\ndata = tomllib.loads(Path(\"pyproject.toml\").read_text(encoding=\"utf-8\"))\nproj = data.get(\"project\", {}) or {}\n\ndeps = list(proj.get(\"dependencies\", []) or [])\ndev = list((proj.get(\"optional-dependencies\", {}) or {}).get(\"dev\", []) or [])\n\n# de-dup while preserving order\nseen = set()\npkgs = []\nfor p in deps + dev:\n if p not in seen:\n pkgs.append(p)\n seen.add(p)\n\nif pkgs:\n subprocess.check_call([sys.executable, \"-m\", \"pip\", \"install\", *pkgs])\nelse:\n print(\"[workflows-codex-env] [warn] No dependencies/dev extras found in pyproject.toml.\")\nPY\n\n# -----------------------------\n# Ensure required test packages (the ones your checker flags as missing)\n# -----------------------------\nlog \"Ensuring required test packages are installed...\"\npython - <<'PY'\nimport importlib, subprocess, sys\n\nrequired = {\n \"pytest\": \"pytest\",\n \"coverage\": \"coverage\",\n \"hypothesis\": \"hypothesis\",\n \"pandas\": \"pandas\",\n \"numpy\": \"numpy\",\n \"pydantic\": \"pydantic\",\n \"yaml\": \"PyYAML\",\n \"requests\": \"requests\",\n \"jsonschema\": \"jsonschema\",\n}\n\nmissing = []\nfor mod, pkg in required.items():\n try:\n importlib.import_module(mod)\n except Exception:\n missing.append(pkg)\n\nif missing:\n print(\"[workflows-codex-env] Installing missing:\", \" \".join(missing))\n subprocess.check_call([sys.executable, \"-m\", \"pip\", \"install\", *missing])\nelse:\n print(\"[workflows-codex-env] Required packages already present.\")\nPY\n\n# -----------------------------\n# Make local modules importable (agents/, templates/, etc.)\n# -----------------------------\nexport PYTHONPATH=\"${REPO_ROOT}${PYTHONPATH:+:${PYTHONPATH}}\"\n\n# Persist env for interactive shells (best-effort)\nMARKER=\"# >>> Workflows Codex env >>>\"\nif [[ -w \"${HOME}/.bashrc\" ]] && ! grep -qs \"${MARKER}\" \"${HOME}/.bashrc\"; then\n {\n echo \"\"\n echo \"${MARKER}\"\n echo \"export WORKFLOWS_REPO_ROOT=\\\"${REPO_ROOT}\\\"\"\n echo \"export VIRTUAL_ENV=\\\"${REPO_ROOT}/.venv\\\"\"\n echo \"export PATH=\\\"${REPO_ROOT}/.venv/bin:\\$PATH\\\"\"\n echo \"export PYTHONPATH=\\\"${REPO_ROOT}\\${PYTHONPATH:+:\\$PYTHONPATH}\\\"\"\n echo \"# <<< Workflows Codex env <<<\"\n } >> \"${HOME}/.bashrc\" || true\nfi\n\n# -----------------------------\n# Optional: run repo dependency checker (should be clean now; don't brick setup if it isn't)\n# -----------------------------\nif [[ -x \"${REPO_ROOT}/scripts/check_test_dependencies.sh\" ]]; then\n log \"Running scripts/check_test_dependencies.sh (non-fatal)\"\n bash \"${REPO_ROOT}/scripts/check_test_dependencies.sh\" || true\nfi\n\nlog \"Setup complete. Common next commands:\"\nlog \" ./scripts/dev_check.sh\"\nlog \" ./scripts/validate_fast.sh\"\n","mode","on","preset_allowlist","allowlist_domains","pypi.org, github.com, files.pythonhosted.org, deb.debian.org, security.ubuntu.com, raw.githubusercontent.com","allowlist_rules","denylist_domains","safe_methods_only","number",695,"https://github.com/stranske/Workflows/pull/695","state","closed","merged","mergeable","draft","title","fix: auto-start coding agent for issue-triggered PRs","body","## Problem\n\nWhen PRs are created from issues (e.g., via `verify:create-issue` label), the Issue Intake workflow in consumer repos was always passing `post_agent_comment: false`, preventing the coding agent from automatically starting work.\n\nThis caused PRs to be stuck in `agent-run-skipped` state because:\n1. Issue event triggers have undefined `inputs`\n2. Template evaluates `inputs.post_codex_comment && 'true' || 'false'` → `'false'`\n3. No `@codex start` comment is posted\n4. Keepalive loop skips agent execution\n\n## Solution\n\nChanged the consumer repo template to:\n- Default to `'true'` for issue events (auto-start agent)\n- Respect `inputs.post_codex_comment` only for `workflow_dispatch`\n- Matches the reusable workflow's default behavior\n\n## Impact\n\nAll consumer repos using this template will now auto-start the coding agent when PRs are created from labeled issues, fixing:\n- PRs from verify:create-issue workflow\n- PRs from agent:codex labeled issues\n- Any issue-triggered PR creation\n\n## Testing\n\nTested the logic:\n- Issue event: `post_agent_comment` → `'true'` (auto-start)\n- Manual dispatch with `post_codex_comment: false`: → `'false'` (no auto-start)\n- Manual dispatch with `post_codex_comment: true`: → `'true'` (auto-start)\n\nResolves the issue affecting:\n- stranske/Portable-Alpha-Extension-Model#1067\n- stranske/Portable-Alpha-Extension-Model#1066 \n- stranske/Trend_Model_Project#4309","base","head","base_sha","d19d5abd25ace26730dec1bf42e22c83d3a4e180","head_sha","head_repo_id","head_repo_full_name","merge_commit_sha","c2564f5bc7df8f132bff5f858c022f4c785275fb","comments","diff","user",{"_266":267,"_159":267,"_313":-5,"_270":271,"_53":268},"commits",1,"changed_files","additions","deletions","email","events",[],[],"messages",[],{"_104":522,"_108":105,"_358":523},{"_104":344,"_345":346},{"_104":322,"_323":324,"_325":326,"_327":328,"_329":-5},"pr","pr_title","fix: default post_agent_comment for issue events","pr_message","### Motivation\n- Issue-triggered PRs were not auto-starting the coding agent because the template evaluated `post_agent_comment` to `'false'` when `inputs` were undefined. \n- This prevented the reusable issue bridge from receiving a `@codex start` activation comment, leaving PRs in `agent-run-skipped` state. \n\n### Description\n- Update the expression that sets `post_agent_comment` in `templates/consumer-repo/.github/workflows/agents-issue-intake.yml` to default to `'true'` for non-dispatch issue events. \n- Change the conditional to only honor `inputs.post_codex_comment` for `workflow_dispatch` by using `github.event_name == 'workflow_dispatch' && (inputs.post_codex_comment == false && 'false' || 'true') || 'true'`. \n- The change ensures issue-created PRs auto-start the coding agent while preserving the manual dispatch behavior. \n- Modified file: `templates/consumer-repo/.github/workflows/agents-issue-intake.yml`.\n\n### Testing\n- No automated tests were run for this template-only change (no CI executed).","output_diff",{"_104":327,"_330":331,"_139":140,"_332":-5,"_305":333,"_334":335,"_336":309,"_337":309,"_338":309,"_339":324,"_340":-5},"pre_apply_patch","repo_id","/workspace/Workflows","preapply_patch_base_commit_sha","diff --git a/templates/consumer-repo/.github/workflows/agents-issue-intake.yml b/templates/consumer-repo/.github/workflows/agents-issue-intake.yml\nindex 23aa7c6ffa25c830f6465ec46af465b36aa11e68..df734d54c8925541ef33ebf52ac22171eb401032 100644\n--- a/templates/consumer-repo/.github/workflows/agents-issue-intake.yml\n+++ b/templates/consumer-repo/.github/workflows/agents-issue-intake.yml\n@@ -156,49 +156,49 @@ jobs:\n const suffix = match[1].toLowerCase();\n return !metadataLabels.has(suffix);\n });\n if (!hasAgentLabel) {\n core.setOutput('should_run', 'false');\n return;\n }\n }\n \n core.setOutput('should_run', 'true');\n core.setOutput('issue_number', issueNumber);\n core.setOutput('agent', agent);\n console.log(`Processing issue #${issueNumber} with agent: ${agent}`);\n \n # Agent bridge mode: Call the Workflows repo reusable issue bridge\n bridge:\n needs: [route, check_labels]\n if: |\n needs.route.outputs.should_run_bridge == 'true' &&\n needs.check_labels.outputs.should_run == 'true'\n uses: stranske/Workflows/.github/workflows/reusable-agents-issue-bridge.yml@main\n with:\n agent: ${{ needs.check_labels.outputs.agent }}\n issue_number: ${{ needs.check_labels.outputs.issue_number }}\n mode: \"create\"\n- post_agent_comment: ${{ github.event_name == 'workflow_dispatch' && (inputs.post_codex_comment && 'true' || 'false') || 'true' }}\n+ post_agent_comment: ${{ github.event_name == 'workflow_dispatch' && (inputs.post_codex_comment == false && 'false' || 'true') || 'true' }}\n agent_pr_draft: ${{ inputs.bridge_draft_pr && 'true' || 'false' }}\n secrets:\n service_bot_pat: ${{ secrets.SERVICE_BOT_PAT }}\n owner_pr_pat: ${{ secrets.OWNER_PR_PAT }}\n WORKFLOWS_APP_ID: ${{ secrets.WORKFLOWS_APP_ID }}\n WORKFLOWS_APP_PRIVATE_KEY: ${{ secrets.WORKFLOWS_APP_PRIVATE_KEY }}\n \n # ChatGPT sync mode: Call the Workflows repo reusable workflow with sync capability\n sync:\n needs: route\n if: needs.route.outputs.should_run_sync == 'true'\n permissions:\n contents: write\n issues: write\n id-token: write\n models: read\n pull-requests: write\n uses: stranske/Workflows/.github/workflows/agents-63-issue-intake.yml@main\n with:\n intake_mode: \"chatgpt_sync\"\n source: ${{ inputs.topic_files }}\n apply_langchain_formatting: ${{ inputs.apply_langchain_formatting && 'true' || 'false' }}\n secrets: inherit\n","external_storage_diff",{"_341":342,"_343":-5},"files_modified","lines_added","lines_removed","commit_message","additional_parent_commit_shas","file_id","file_00000000e16c71f79d681d43d8c3f373","ttl","partial_repo_snapshot","files",[347],{"_348":349,"_350":-5,"_351":352,"_353":-5},"path","templates/consumer-repo/.github/workflows/agents-issue-intake.yml","contents","line_range_contents",[354],"missing_reason",{"_355":309,"_356":357,"_358":359,"_360":70},"line_range_start","line_range_end",204,"content",[361,362,363,364,365,366,367,362,368,369,370,362,371,362,372,373,374,375,213,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,387,395,396,397,387,395,398,399,400,387,401,402,403,404,387,401,405,406,407,387,395,408,409,410,387,401,405,213,411,412,413,414,213,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,213,437,438,439,440,441,442,431,441,439,434,213,443,444,445,446,447,448,449,450,418,419,451,452,453,423,454,455,456,457,458,459,460,461,213,462,463,464,465,466,213,467,468,469,213,470,471,472,473,474,475,476,477,478,479,480,481,213,482,483,474,475,476,477,478,484,485,486,481,487,213,488,489,490,491,213,492,493,494,446,447,495,496,497,498,499,500,501,502,503,504,505,506,507,213,508,509,445,510,511,512,513,514,515,516,517,497,518,519,520,521],"contains_end_of_file","# Thin caller for issue intake - delegates to Workflows repo reusable workflow","#","# Two modes:","# 1. Label-based (agent_bridge): Assigns agents to issues when labeled","# with agent:* labels","# 2. ChatGPT sync (chatgpt_sync): Bulk creates issues from topic files","# with optional LangChain formatting","# Triggers:","# - Issue opened/reopened/labeled with agent:* labels","# - Manual dispatch for both modes","# Copy this file to: .github/workflows/agents-issue-intake.yml","# Required secrets:","# - SERVICE_BOT_PAT: PAT for service bot account (comments, labels)","# - OWNER_PR_PAT: PAT for creating PRs on behalf of repository owner","name: Agents Issue Intake","on:"," issues:"," types:"," - opened"," - reopened"," - labeled"," - unlabeled"," workflow_dispatch:"," inputs:"," mode:"," description: \"Mode: agent_bridge (label-based) or chatgpt_sync (bulk creation)\""," required: false"," type: choice"," options:"," - agent_bridge"," - chatgpt_sync"," default: agent_bridge"," issue_number:"," description: \"[agent_bridge] Issue number to process\""," type: string"," bridge_agent:"," description: \"[agent_bridge] Agent to use (codex, copilot)\""," default: \"codex\""," post_codex_comment:"," description: \"[agent_bridge] Auto-post activation comment\""," type: boolean"," default: true"," bridge_draft_pr:"," description: \"[agent_bridge] Open bootstrap PRs as draft\""," default: false"," topic_files:"," description: \"[chatgpt_sync] Topic files to sync (e.g., topics.json, agents/*.md)\""," default: \"\""," apply_langchain_formatting:"," description: \"[chatgpt_sync] Apply LangChain formatting to created issues\"","permissions:"," contents: write"," issues: write"," pull-requests: write","jobs:"," # Determine which mode to run"," route:"," runs-on: ubuntu-latest"," outputs:"," mode: ${{ steps.determine.outputs.mode }}"," should_run_bridge: ${{ steps.determine.outputs.should_run_bridge }}"," should_run_sync: ${{ steps.determine.outputs.should_run_sync }}"," steps:"," - name: Determine mode"," id: determine"," run: |"," echo \"DEBUG: event_name=${{ github.event_name }}\""," echo \"DEBUG: inputs.mode=${{ inputs.mode }}\""," if [[ \"${{ github.event_name }}\" == \"workflow_dispatch\" ]]; then"," mode=\"${{ inputs.mode || 'agent_bridge' }}\""," else"," # Issue events always use agent_bridge mode"," mode=\"agent_bridge\""," fi"," echo \"DEBUG: final mode=${mode}\""," echo \"mode=${mode}\" >> $GITHUB_OUTPUT"," if [[ \"${mode}\" == \"agent_bridge\" ]]; then"," echo \"should_run_bridge=true\" >> $GITHUB_OUTPUT"," echo \"should_run_sync=false\" >> $GITHUB_OUTPUT"," elif [[ \"${mode}\" == \"chatgpt_sync\" ]]; then"," echo \"should_run_bridge=false\" >> $GITHUB_OUTPUT"," echo \"should_run_sync=true\" >> $GITHUB_OUTPUT"," # Gate for agent_bridge mode: only proceed if issue has agent:* or agents:* label"," check_labels:"," needs: route"," if: |"," needs.route.outputs.should_run_bridge == 'true' &&"," (github.event_name != 'issues' ||"," contains(toJson(github.event.issue.labels.*.name), 'agent:') ||"," contains(toJson(github.event.issue.labels.*.name), 'agents:'))"," should_run: ${{ steps.check.outputs.should_run }}"," issue_number: ${{ steps.check.outputs.issue_number }}"," agent: ${{ steps.check.outputs.agent }}"," - name: Check labels and extract info"," id: check"," uses: actions/github-script@v8"," with:"," script: |"," const eventName = context.eventName;"," let issueNumber = '${{ inputs.issue_number }}' || '';"," let agent = '${{ inputs.bridge_agent }}' || 'codex';"," // Metadata labels that aren't actual agent assignments"," const metadataLabels = new Set(["," 'keepalive', 'formatted', 'optimize', 'allow-change',"," 'apply-suggestions', 'debug', 'format', 'sync-failed', 'sync-required'"," ]);"," if (eventName === 'issues') {"," const issue = context.payload.issue;"," issueNumber = String(issue.number);"," // Extract agent from labels (agent:codex, agents:codex, etc.)"," // Skip metadata labels that aren't actual agent assignments"," const labels = issue.labels.map(l => l.name);"," const agentLabel = labels.find(l => {"," const match = l.match(/^agents?:([a-z-]+)$/i);"," if (!match) return false;"," const 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